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Changes in nucleosome formation at gene promoters in the archiascomycetous yeast Saitoella complicata

  • Received: 08 December 2016 Accepted: 09 March 2017 Published: 16 March 2017
  • We measured the degree of nucleosome formation at the gene promoters in trichostatin A-treated (1, 2, and 3 μg/mL) cells of the archiascomycete Saitoella complicata and those in enlarged S. complicata cells after zymolyase treatment. TSA-treated and enlarged cells showed similar changes in nucleosome occupancy in five out of six positions in the gene promoters. These results suggest that changes in nucleosome formation at the gene promoters could serve as stress response mechanisms elicited in response to spheroplast (zymolyase treatment) and TSA treatment. In addition, we demonstrated that changes in nucleosome position occurred mainly in cells treated with 1 μg/mL TSA, whereas cells treated with 2 and 3 μg/mL TSA did not exhibit significant changes in the degree of nucleosome formation.

    Citation: Hikaru Nakamiya, Saeka Ijima, Hiromi Nishida. Changes in nucleosome formation at gene promoters in the archiascomycetous yeast Saitoella complicata[J]. AIMS Microbiology, 2017, 3(2): 136-142. doi: 10.3934/microbiol.2017.2.136

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  • We measured the degree of nucleosome formation at the gene promoters in trichostatin A-treated (1, 2, and 3 μg/mL) cells of the archiascomycete Saitoella complicata and those in enlarged S. complicata cells after zymolyase treatment. TSA-treated and enlarged cells showed similar changes in nucleosome occupancy in five out of six positions in the gene promoters. These results suggest that changes in nucleosome formation at the gene promoters could serve as stress response mechanisms elicited in response to spheroplast (zymolyase treatment) and TSA treatment. In addition, we demonstrated that changes in nucleosome position occurred mainly in cells treated with 1 μg/mL TSA, whereas cells treated with 2 and 3 μg/mL TSA did not exhibit significant changes in the degree of nucleosome formation.


    Consider the following mth degree homogeneous polynomial of n variables f(x) as

    f(x)=i1,i2,,imNai1i2imxi1xi2xim, (1.1)

    where x=(x1,x2,,xn)Rn. When m is even, f(x) is called positive definite if

    f(x)>0,foranyxRn,x0.

    The homogeneous polynomial f(x) in (1.1) can be expressed as the tensor product of a symmetric tensor A with m-order, n-dimension and xm defined by

    f(x)Axm=i1,i2,,imNai1i2imxi1xi2xim, (1.2)

    where

    A=(ai1i2im),ai1i2imC(R),ij=1,2,,n,j=1,2,,m,

    C(R) presents complex (real) number fields. The symmetric tensor A is called positive definite if f(x) in (1.2) is positive definite [1]. Moreover, a tensor I=(δi1i2im) is called the unit tensor[2], where

    δi1i2im={1,ifi1==im,0,otherwise.

    The positive definiteness of tensor has received much attention of researchers' in recent decade [3,4,5]. Based on the Sturm theorem, the positive definiteness of a multivariate polynomial form can be checked for n3 [6]. For n>3 and m4, it is difficult to determine the positive definiteness of f(x) in (2). Ni et al.[1] provided an eigenvalue method for identifying positive definiteness of a multivariate form. However, all the eigenvalues of the tensor are needed in this method, thus the method is not practical when tensor order or dimension is large.

    Recently, based on the criteria of H-tensors, Li et al.[7] provided a practical method for identifying the positive definiteness of an even-order symmetric tensor. H-tensor is a special kind of tensors and an even order symmetric H-tensor with positive diagonal entries is positive definite. Due to this, we may identify the positive definiteness of a tensor via identifying H-tensor. For the latter, with the help of generalized diagonally dominant tensor, various criteria for H-tensors and M-tensors is established [8,9,10,11,12,13,14,15,16], which only depends on the elements of the tensors and is more effective to determine whether a given tensor is an H-tensor (M-tensor) or not. For example, the following result is given in [16]:

    Theorem 1. Let A=(ai1im) be a complex tensor with m-order, n-dimension. If

    |aiii|>i2,i3,,imNm1Nm13δii2im=0|aii2im|+i2i3imNm13maxj{i2,i3,,im}Λj(A)|ajjj||aii2im|,    iN1N2,

    then A is an H-tensor.

    In this paper, we continue to present new criterions based on H-tensors for identifying positive definiteness of homogeneous polynomial forms. The obtained results extend the corresponding conclusions [16,17,18]. The validity of our proposed methods are theoretically guaranteed and the numerical experiments show their effciency.

    In this section, some notation, definitions and lemmas are given.

    Let S be a nonempty subset of N={1,2,,n} and let NS be the complement of S in N. Given an m-order n-dimension complex tensor A=(ai1im), we denote

    Λi(A)=i2,,imNδii2im=0|aii2im|=i2,,imN|aii2im||aiii|;N1=N1(A)={iN:0<|aiii|=Λi(A)};N2=N2(A)={iN:0<|aiii|<Λi(A)};N3=N3(A)={iN:|aiii|>Λi(A)};Nm10=Nm1(Nm12Nm13);q=maxiN2Λi(A)|aiii|Λi(A);Pi(A)=q(i2,,imNm10|aii2im|+i2,,imNm12|aii2im|+i2,,imNm13δii2im=0|aii2im|),iN3;t=maxiN3q(i2imNm10|aii2im|+i2imNm12|aii2im|)Pi(A)i2imNm13δii2im=0maxj{i2,i3,,im}Pj(A)|ajjj||aii2im|.

    In this paper, we always assume that neither N1 or N2 is empty. Otherwise, we assume that A satisfies: aiii0,Λi(A)0,iN.

    we may define the following structured tensors extended from matrices.

    Definition 1. [10] Let A=(ai1i2im) be an m-order n-dimension complex tensor. A is called an H-tensor if there is a positive vector x=(x1,x2,,xn)TRn such that

    |aiii|xm1i>i2,,imNδii2im=0|aii2im|xi2xim,iN.

    Definition 2. [2] An m-order n-dimension complex tensor A=(ai1i2im) is called reducible if there exists a nonempty proper index subset IN such that

    ai1i2im=0,i1I,i2,,imI.

    Otherwise, we say A is irreducible.

    Example 1. Consider the 4-order 4-dimension tensor A given

    a1111=a2222=a3333=a4444=a1444=a2333=2,

    and zero elsewhere. Then ai1i2i3i4=0 for all i1{1,4} and for all i2,i3,i4{2,3}. From Definition 2, we have that A is reducible.

    Definition 3. [12] Let A=(ai1i2im) be an m-order n-dimension complex tensor, for i,jN(ij), if there exist indices k1,k2,,kr with

    i2,,imNδksi2im=0,ks+1{i2,,im}|aksi2im|0,s=0,1,,r,

    where k0=i,kr+1=j, we call that there is a nonzero elements chain from i to j.

    It is shown that for any H-tensor, there exists at least one strictly diagonally dominant row [7]. Further, we have the following conclusion.

    Lemma 1. [10] If A is a strictly diagonally dominant tensor, then A is an H-tensor.

    Lemma 2. [7] Let A=(ai1im) be a complex tensor with m-order, n-dimension. If there exists a positive diagonal matrix X such that AXm1 is an H-tensor, then A is an H-tensor.

    Lemma 3. [7] Let A=(ai1im) be a complex tensor with m-order, n-dimension. If A is irreducible,

    |aii|Λi(A),iN,

    and strictly inequality holds for at least one i, then A is an H-tensor.

    Lemma 4. [12] Let A=(ai1im) be a complex tensor with m-order, n-dimension. If

    (i) |aiii|Λi(A),iN,

    (ii) N3={iN:|aiii|>Λi(A)},

    (iii) For any iN3, there exists a nonzero elements chain from i to j such that jN3,

    then A is an H-tensor.

    In this section, we give some new criteria for H-tensors.

    Theorem 2. Let A=(ai1im) be a complex tensor with m-order, n-dimension. If for iN2,

    |aiii|>Λi(A)Λi(A)|aiii|[q(i2i3imNm10|aii2im|+i2i3imNm12δii2im=0|aii2im|)+i2i3imNm13maxj{i2,i3,,im}tPj(A)|ajjj||aii2im|], (3.1)

    and for iN1, |aiii|i2i3imNm10δii2im=0|aii2im|, then A is an H-tensor.

    Proof. From the definition of q, we know that 0q<1, qΛi(A)|aiii|Λi(A)(iN2), so for any iN3,

    Pi(A)=q(i2,,imNm10|aii2im|+i2,,imNm12|aii2im|+i2,,imNm13δii2im=0|aii2im|)=qΛi(A)<q|aiii|,

    that is

    q>Pi(A)|aiii|. (3.2)

    By the definition of Pi(A), we have

    q(i2i3imNm10|aii2im|+i2i3imNm12|aii2im|)Pi(A)i2i3imNm13δii2im=0maxj{i2,i3,,im}Pj(A)|ajjj||aii2im|=Pi(A)qi2imNm13δii2im=0|aii2im|Pi(A)i2i3imNm13δii2im=0maxj{i2,i3,,im}Pj(A)|ajjj||aii2im|1.

    For any iN3, from Inequality (3.2) and 0t1, we conclude that

    q>tPi(A)|aiii|,iN3. (3.3)

    For any iN2, by Inequality (3.1), it holds that

    |aiii|Λi(A)|aiii|Λi(A)>q(i2imNm10|aii2im|+i2imNm12δii2im=0|aii2im|)+i2imNm13maxj{i2,i3,,im}tPj(A)|ajjj||aii2im|. (3.4)

    By Inequality (3.3) and Inequality (3.4), there exists a sufficiently small positive number ε such that

    q>tPi(A)|aiii|+ε,iN3, (3.5)

    and

    |aiii|Λi(A)|aiii|Λi(A)>q(i2imNm10|aii2im|+i2imNm12δii2im=0|aii2im|)+i2imNm13maxj{i2,i3,,im}tPj(A)|ajjj||aii2im|+εi2imNm13|aii2im|,iN2,

    that is,

    εi2imNm13|aii2im|<|aiii|Λi(A)|aiii|Λi(A)q(i2imNm10|aii2im|+i2imNm12δii2im=0|aii2im|)i2imNm13maxj{i2,i3,,im}tPj(A)|ajjj||aii2im|iN2. (3.6)

    By the definition of t, it holds that

    tq(i2imNm10|aii2im|+i2imNm12|aii2im|)Pi(A)i2imNm13δii2im=0maxj{i2,i3,,im}Pj(A)|ajjj||aii2im|,iN2,

    that is

    q(i2imNm10|aii2im|+i2imNm12|aii2im|)+ti2imNm13δii2im=0maxj{i2,i3,,im}Pj(A)|ajjj||aii2im|tPi(A),iN2. (3.7)

    Let the matrix D=diag(d1,d2,,dn), and denote B=ADm1=(bi1i2im), where

    di={q1m1,iN1,(Λi(A)|aiii|Λi(A))1m1,iN2,(ε+tPi(A)|aiii|)1m1,iN3.

    For any iN1, by q>tPi(A)|aiii|(iN3), we conclude that

    Λi(B)=qi2imNm10δii2im=0|aii2im|+i2imNm12|aii2im|(Λi2(A)|ai2i2i2|Λi2(A))1m1(Λim(A)|aimimim|Λim(A))1m1+i2imNm13|aii2im|(tPi2(A)|ai2i2i2|+ε)1m1(tPim(A)|aimimim|+ε)1m1q(i2imNm10δii2im=0|aii2im|+i2imNm12|aii2im|)+i2imNm13|aii2im|(maxj{i2,i3,,im}tPj(A)|ajjj|+ε)<q(i2imNm10δii2im=0|aii2im|+i2imNm12|aii2im|)+qi2imNm13|aii2im|=q|aiii|=|biii|.

    For iN2, by Inequality (3.6), then

    Λi(B)=qi2imNm10|aii2im|+i2imNm12δii2im=0|aii2im|(Λi2(A)|ai2i2i2|Λi2(A))1m1(Λim(A)|aimimim|Λim(A))1m1+i2imNm13|aii2im|(tPi2(A)|ai2i2i2|+ε)1m1(tPim(A)|aimimim|+ε)1m1q(i2imNm10|aii2im|+i2imNm12δii2im=0|aii2im|)+i2imNm13|aii2im|(maxj{i2,i3,,im}tPj(A)|ajjj|+ε)=q(i2imNm10|aii2im|+i2imNm12δii2im=0|aii2im|)+i2imNm13maxj{i2,i3,,im}tPj(A)|ajjj||aii2im|+εi2imNm13|aii2im|<q(i2imNm10|aii2im|+i2imNm12δii2im=0|aii2im|)+i2imNm13maxj{i2,i3,,im}tPj(A)|ajjj||aii2im|+[|aiii|Λi(A)|aiii|Λi(A)q(i2imNm10|aii2im|+i2imNm12δii2im=0|aii2im|)i2imNm13maxj{i2,i3,,im}tPj(A)|ajjj||aii2im|]=|aiii|Λi(A)|aiii|Λi(A)=|biii|.

    Finally, for any iN3, by Inequality (3.7), thus

    Λi(B)=qi2imNm10|aii2im|+i2imNm12|aii2im|(Λi2(A)|ai2i2i2|Λi2(A))1m1(Λim(A)|aimimim|Λim(A))1m1+i2imNm13δii2im=0|aii2im|(tPi2(A)|ai2i2i2|+ε)1m1(tPim(A)|aimimim|+ε)1m1q(i2imNm10|aii2im|+i2imNm12|aii2im|)+i2imNm13δii2im=0|aii2im|(maxj{i2,i3,,im}tPj(A)|ajjj|+ε)=q(i2imNm10|aii2im|+i2imNm12|aii2im|)+i2imNm13δii2im=0maxj{i2,i3,,im}tPj(A)|ajjj||aii2im|+εi2imNm13δii2im=0|aii2im|tPi(A)+εi2imNm13δii2im=0|aii2im|<tPi(A)+ε|aiii|=|biii|.

    Therefore, we obtain that |biii|>Λi(B)(iN). From Lemma 1, B is an H-tensor. Further, by Lemma 2, A is an H-tensor.

    Remark 1. From Theorem 2, we conclude that 0p<1, 0t1, and for any iN3,

    tPi(A)|aiii|<Λi(A)|aiii|<1.

    Thus, all conditions in Theorem 2 are weaker than that in Theorem 1. Example 2 illustrates the superiority of Theorem 2.

    Theorem 3. Let A=(ai1im) be a complex tensor with m-order, n-dimension. If A is irreducible, and for all iN2,

    |aiii|Λi(A)Λi(A)|aiii|[q(i2i3imNm10|aii2im|+i2i3imNm12δii2im=0|aii2im|)+i2i3imNm13maxj{i2,i3,,im}tPj(A)|ajjj||aii2im|], (3.8)

    and at least one strict inequality in (3.8) holds, then A is an H-tensor.

    Proof. Notice that A is irreducible, this implies that for any iN3, Pi(A)>0t>0 (Otherwise, A is reducible).

    For any iN2, by Inequality (3.8), we obtain

    |aiii|Λi(A)|aiii|Λi(A)q(i2i3imNm10|aii2im|+i2i3imNm12δii2im=0|aii2im|)+i2i3imNm13maxj{i2,i3,,im}tPj(A)|ajjj||aii2im|. (3.9)

    Let the matrix D=diag(d1,d2,,dn), denote B=ADm1=(bi1i2im), where

    di={q1m1,iN1,(Λi(A)|aiii|Λi(A))1m1,iN2,(tPi(A)|aiii|)1m1,iN3.

    For any iN1, by q>tPi(A)|aiii|(iN3), we conclude that

    Λi(B)=qi2imNm10δii2im=0|aii2im|+i2imNm12|aii2im|(Λi2(A)|ai2i2i2|Λi2(A))1m1(Λim(A)|aimimim|Λim(A))1m1+i2imNm13|aii2im|(tPi2(A)|ai2i2i2|)1m1(tPim(A)|aimimim|)1m1q(i2imNm10δii2im=0|aii2im|+i2imNm12|aii2im|)+i2imNm13maxj{i2,i3,,im}tPj(A)|ajjj||aii2im|<q(i2imNm10δii2im=0|aii2im|+i2imNm12|aii2im|)+qi2imNm13|aii2im|=q|aiii|=|biii|.

    For any iN2, by Inequality (3.9), it holds that

    Λi(B)=qi2imNm10|aii2im|+i2imNm12δii2im=0|aii2im|(Λi2(A)|ai2i2i2|Λi2(A))1m1(Λim(A)|aimimim|Λim(A))1m1+i2imNm13|aii2im|(tPi2(A)|ai2i2i2|)1m1(tPim(A)|aimimim|)1m1q(i2imNm10|aii2im|+i2imNm12δii2im=0|aii2im|)+i2imNm13maxj{i2,i3,,im}tPj(A)|ajjj||aii2im||aiii|Λi(A)|aiii|Λi(A)=|biii|.

    Next, for any iN3, by Inequality (3.7), then

    Λi(B)=qi2imNm10|aii2im|+i2imNm12|aii2im|(Λi2(A)|ai2i2i2|Λi2(A))1m1(Λim(A)|aimimim|Λim(A))1m1+i2imNm13δii2im=0|aii2im|(tPi2(A)|ai2i2i2|)1m1(tPim(A)|aimimim|)1m1q(i2imNm10|aii2im|+i2imNm12|aii2im|)+i2imNm13δii2im=0maxj{i2,i3,,im}tPj(A)|ajjj||aii2im|tPi(A)=tPi(A)|aiii|×|aiii|=|biii|.

    Therefore, |biii|Λi(B) (iN), and for all iN2, at least one strict inequality in (10) holds, that is, there exists an i0N2 such that |bi0i0i0|>Λi0(B).

    On the other hand, since A is irreducible and so is B. Then, by Lemma 3, we have that B is an H-tensor. By Lemma 2, A is also an H-tensor.

    Let

    K(A)={iN2:|aiii|>Λi(A)Λi(A)|aiii|[q(i2i3imNm10|aii2im|+i2i3imNm12δii2im=0|aii2im|)+i2i3imNm13maxj{i2,i3,,im}tPj(A)|ajjj||aii2im|]}.

    Theorem 4. Let A=(ai1im) be a complex tensor with m-order, n-dimension. For any iN2,

    |aiii|Λi(A)Λi(A)|aiii|[q(i2i3imNm10|aii2im|+i2i3imNm12δii2im=0|aii2im|)+i2i3imNm13maxj{i2,i3,,im}tPj(A)|ajjj||aii2im|],

    and if for any iNK(A), there exists a nonzero elements chain from i to j such that jK(A), then A is an H-tensor.

    Proof. Let the matrix D=diag(d1,d2,,dn), and denote B=ADm1=(bi1i2im), where

    di={q1m1,iN1,(Λi(A)|aiii|Λi(A))1m1,iN2,(tPi(A)|aiii|)1m1,iN3.

    A similar argument to that of Theorem 2, we can prove that |biii|Λi(B)(iN), and there exists at least an iN2 such that |biii|>Λi(B).

    On the other hand, if |biii|=Λi(B), then iNK(A), by the assumption, we know that there exists a nonzero elements chain of A from i to j, such that jK(A). Hence, there exists a nonzero elements chain of B from i to j, such that j satisfying |bjjj|>Λj(B).

    Based on above analysis, we get that B satisfies the conditions of Lemma 4, so B is an H-tensor. By Lemma 2, A is an H-tensor.

    Example 2. Consider the 3-order 3-dimension tensor A=(aijk) defined as follows:

    A=[A(1,:,:),A(2,:,:),A(3,:,:)],
    A(1,:,:)=(12101601015),A(2,:,:)=(110060001),A(3,:,:)=(1000100016).

    Obviously,

    |a111|=12,  Λ1(A)=24,  |a222|=6,  Λ2(A)=3,  |a333|=16,  Λ3(A)=2.

    so N1=,N2={1},N3={2,3}. By calculations, we have

    qi=1=241224=12=q,     
    P2(A)=12(1+1+1)=32,     P3(A)=12(0+1+1)=1,
    P2(A)|a222|=326=14,     P3(A)|a333|=116,
    ti=2=12(1+1)3214×1=45,     ti=3=12(0+1)114×1=23,     t=45.

    When i=1, we get

    Λ1(A)Λ1(A)|a111|[q(i2i3N20|a1i2i3|+i2i3N22δ1i2i3=0|a1i2i3|)+i2i3N23maxj{i2,i3}tPj(A)|ajjj||a1i2i3|]=242412[12(3+0)+45×14×21]=575<12=|a111|,

    so A satisfies the conditions of Theorem 2, then A is an H-tensor. However,

    i2i3N2N23δ1i2i3=0|a1i2i3|+i2i3N23maxj{i2,i3}Λj(A)|ajjj||a1i2i3|=3+12×21=272>12=|a111|,

    so A does not satisfy the conditions of Theorem 1.

    Based on the criteria of H-tensors in Section 3, we present some criteria for identifying the positive definiteness of an even-order real symmetric tensor. First, we recall the following lemma.

    Lemma 5. [7] Let A=(ai1i2im) be an even-order real symmetric tensor with m-order, n-dimension, and akk>0 for all kN. If A is an H-tensor, then A is positive definite.

    From Theorems 24 and Lemma 5, we obtain easily the following result.

    Theorem 5. Let A=(ai1i2im) be an even-order real symmetric tensor with m-order, n-dimension, and aiii>0 for all iN. If one of the following holds:

    (i) A satisfies all the conditions of Theorem 2,

    (ii) A satisfies all the conditions of Theorem 3,

    (iii) A satisfies all the conditions of Theorem 4,

    then A is positive definite.

    Example 3. Let

    f(x)=Ax4=16x41+20x42+30x43+33x448x31x4+12x21x2x312x2x23x424x1x2x3x4

    be a 4th-degree homogeneous polynomial. We can get the 4-order 4-dimension real symmetric tensor A=(ai1i2i3i4), where

    a1111=16,  a2222=20,  a3333=30,  a4444=33,a1114=a1141=a1411=a4111=2,a1123=a1132=a1213=a1312=a1231=a1321=1,a2113=a2131=a2311=a3112=a3121=a3211=1,a2334=a2343=a2433=a4233=a4323=a4332=1,a3234=a3243=a3324=a3342=a3423=a3432=1,a1234=a1243=a1324=a1342=a1423=a1432=1,a2134=a2143=a2314=a2341=a2413=a2431=1,a3124=a3142=a3214=a3241=a3412=a3421=1,a4123=a4132=a4213=a4231=a4312=a4321=1,

    and zero elsewhere. By calculations, we have

    a1111=16<18=Λ1(A),

    and

    a4444(a1111Λ1(A)+|a1444|)=66<0=Λ4(A)|a1444|.

    Then A is not strictly diagonally dominate as defined in [17] or quasidoubly strictly diagonally dominant as defined in [18]. Hence, we cannot use Theorem 3 in [17] and Theorem 4 in [18] to identify the positive definiteness of A. However, it can be verified that A satisfies all the conditions of Theorem 2.

    Λ1(A)=18,  Λ2(A)=12,  Λ3(A)=15,  Λ4(A)=11,

    so N1=,N2={1},N3={2,3,4}. By calculations, we have

    qi=1=181618=19=q,     
    P2(A)=19(9+0+3)=43,     P3(A)=19(9+0+6)=53,     P4(A)=19(6+2+3)=119,
    P2(A)|a2222|=4320=115,     P3(A)|a3333|=5330=118,     P4(A)|a4444|=11933=127,
    ti=2=19(9+0)43115×3=1517,     ti=3=19(9+1)53115×6=1519,
    ti=4=19(6+2)119115×3=1013,     t=1517.

    When i=1, we get

    Λ1(A)Λ1(A)|a1111|[q(i2i3i4N30|a1i2i3i4|+i2i3i4N32δ1i2i3i4=0|a1i2i3i4|)+i2i3i4N33maxj{i2,i3,i4}tPj(A)|ajjjj||a1i2i3i4|]=181816[19(12+0)+1517×115×6]=25817<16=|a1111|.

    Therefore, from Theorem 5, we have that A is positive definite, that is, f(x) is positive definite.

    In this paper, we given some inequalities to identify whether a tensor is an H-tensor, which was also used to identify the positive definiteness of an even degree homogeneous polynomial f(x)Axm. These inequalities were expressed in terms of the elements of A, so they can be checked easily.

    The authors wish to give their sincere thanks to the anonymous referees for their valuable suggestions and helpful comments, which help improve the quality of the paper significantly. This work was supported by the National Natural Science Foundation of China (11861077), the Foundation of Science and Technology Department of Guizhou Province (20191161, 20181079), the Talent Growth Project Department of Guizhou Province ([2016]168) and the Research Foundation of Guizhou Minzu University (2019YB08).

    The authors declare that they have no competing interests.

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